It's not like planes crashing into government buildings (via Kamekaze rather than jihadi) wasn't out there in the popular fiction. Clancy also had a plot line about attacking Wall Street. It takes a complete lack of imagination to not check popular fiction plot lines for possible threats when you believe we are in a state of war against terrorists.
Condi Rice could have been told directly about 9/11 plans by Bin Laden himself, and she would have thought it too fantastic to believe, and too inflammatory to bring to Bush. National Security Advisors are supposed to have a bit of paranoia about them. Condi can't seem to believe anything really bad about anybody.
With regards to 9/11, Bush chose Rice as his NSA in part because she was an recognized expert on terrorism. She gave speeches on the threat of Islamic terrorism and I believe Bush even made it a campaign issue in 2000. During her first few months on the job she wrote a plan to go after Al Qaeda which was on President Bush's desk on 9/10/01 for his review.